Contacts of the strand formed by residues 120 - 125 (chain B) in PDB entry 2PWY
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 120 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B MET 3.0 7.9 + - - +
96B ARG* 3.1 43.5 - - + +
97B VAL* 2.9 29.3 + - - +
115B VAL* 3.6 3.5 - - - +
119B GLY* 1.3 75.3 - - - +
121B VAL* 1.3 77.9 + - - +
122B GLU* 3.1 16.2 - - - +
146B ASN* 3.3 15.0 - - - +
148B ARG* 3.5 50.0 - - + +
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B VAL* 3.5 9.6 - - + +
99B GLU* 4.2 14.1 - - + +
108B THR* 4.3 11.7 - - + +
111B LEU* 3.8 31.4 - - + -
112B ALA* 3.6 40.2 - - + +
115B VAL* 3.9 6.7 - - + -
120B LEU* 1.3 78.4 - - - +
122B GLU* 1.3 57.7 + - - +
123B SER* 3.7 7.1 + - - -
146B ASN 2.8 10.2 + - - +
147B VAL* 3.5 10.1 - - + +
148B ARG 2.8 31.7 + - - +
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Residues in contact with GLU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ARG* 2.6 33.2 + - - -
97B VAL 2.9 8.9 + - - +
98B LEU* 3.4 6.8 - - + +
99B GLU 2.8 24.8 + - - +
120B LEU* 3.1 17.8 - - + +
121B VAL* 1.3 71.1 - - - +
123B SER* 1.3 58.4 + - - +
124B TYR* 4.2 11.2 - - + +
148B ARG* 3.2 26.2 + - - +
150B HIS* 2.7 33.9 + - + +
164B TYR* 3.4 31.2 - - + +
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Residues in contact with SER 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B GLU* 2.7 34.0 + - - -
102B THR* 2.7 29.0 + - - +
108B THR* 4.6 0.4 - - - -
121B VAL* 3.7 8.3 + - - -
122B GLU* 1.3 72.1 - - - +
124B TYR* 1.3 58.2 + - - +
147B VAL* 4.5 4.9 - - - -
148B ARG 2.9 13.7 + - - +
149B PHE* 3.5 14.1 - - - -
150B HIS* 2.8 32.6 + - - +
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Residues in contact with TYR 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502A SAH 4.2 1.8 - - + -
98B LEU* 3.7 26.0 - - + -
99B GLU 2.8 13.6 + - - +
100B ALA* 3.6 10.9 - - + +
101B GLY* 3.2 10.6 - - - -
102B THR* 2.9 21.8 + - - -
122B GLU* 4.1 4.5 - - + +
123B SER* 1.3 75.0 - - - +
125B GLU* 1.3 60.6 + - - +
150B HIS* 3.3 46.6 + + + -
151B LEU 5.6 1.1 - - - -
152B GLY* 4.1 16.4 - - - +
153B LYS 4.6 4.9 - - - -
154B LEU* 3.8 19.7 - - + -
157B ALA* 3.4 28.5 - - + +
158B GLU 4.3 6.2 + - - -
159B LEU* 3.4 19.0 - - + +
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Residues in contact with GLU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502A SAH 2.6 54.2 + - - -
102B THR* 3.4 17.7 + - - +
103B GLY 2.8 19.3 + - - +
124B TYR* 1.3 75.0 - - - +
126B ALA* 1.3 63.1 + - - +
127B ARG* 2.9 35.8 + - - +
130B HIS* 3.6 6.7 - - + -
131B LEU* 3.6 26.2 - - + +
150B HIS 3.0 6.7 + - - -
151B LEU* 3.4 11.4 - - - +
152B GLY 2.9 20.3 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il